******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.3.3 (Release date: Sun Feb 7 15:39:52 2021 -0800) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://meme-suite.org. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** PRIMARY SEQUENCES= ../result/final_prediction/worm/fasta/RankLinear2.0_40/unc-30.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrIV:5054449-5054529 1.0000 80 chrX:2604759-2604839 1.0000 80 chrII:14427890-14427970 1.0000 80 chrIII:5571237-5571317 1.0000 80 chrI:13495264-13495344 1.0000 80 chrIV:1070516-1070596 1.0000 80 chrX:3898588-3898668 1.0000 80 chrIV:1057899-1057979 1.0000 80 chrIV:7899066-7899146 1.0000 80 chrV:4775283-4775363 1.0000 80 chrI:7952195-7952275 1.0000 80 chrV:4468462-4468542 1.0000 80 chrIII:13466366-13466446 1.0000 80 chrX:4095126-4095206 1.0000 80 chrII:3270702-3270782 1.0000 80 chrIV:2725927-2726007 1.0000 80 chrV:1471779-1471859 1.0000 80 chrIV:14033232-14033312 1.0000 80 chrIV:9811695-9811775 1.0000 80 chrI:10033694-10033774 1.0000 80 chrIV:11765749-11765829 1.0000 80 chrIV:17281424-17281504 1.0000 80 chrX:13913845-13913925 1.0000 80 chrI:13514361-13514441 1.0000 80 chrII:156129-156209 1.0000 80 chrX:11137844-11137924 1.0000 80 chrII:13237916-13237996 1.0000 80 chrIV:14464276-14464356 1.0000 80 chrV:5201851-5201931 1.0000 80 chrI:12170852-12170932 1.0000 80 chrV:6224582-6224662 1.0000 80 chrIII:1202352-1202432 1.0000 80 chrI:7370268-7370348 1.0000 80 chrI:11140623-11140703 1.0000 80 chrV:18079287-18079367 1.0000 80 chrI:8786917-8786997 1.0000 80 chrI:1691548-1691628 1.0000 80 chrII:1233092-1233172 1.0000 80 chrIV:443759-443839 1.0000 80 chrV:18087022-18087102 1.0000 80 chrII:7945300-7945380 1.0000 80 chrIV:12724765-12724845 1.0000 80 chrIII:10881844-10881924 1.0000 80 chrIV:15471544-15471624 1.0000 80 chrIII:13061296-13061376 1.0000 80 chrI:17002-17082 1.0000 80 chrV:904827-904907 1.0000 80 chrV:265214-265294 1.0000 80 chrX:949603-949683 1.0000 80 chrII:8185168-8185248 1.0000 80 chrI:11517247-11517327 1.0000 80 chrIII:10634167-10634247 1.0000 80 chrII:411000-411080 1.0000 80 chrI:27165-27245 1.0000 80 chrV:10356110-10356190 1.0000 80 chrIV:14034130-14034210 1.0000 80 chrIV:2177689-2177769 1.0000 80 chrI:535370-535450 1.0000 80 chrIII:12612578-12612658 1.0000 80 chrII:6951536-6951616 1.0000 80 chrV:9175423-9175503 1.0000 80 chrV:5592443-5592523 1.0000 80 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme -oc ../result/final_prediction/worm/inference_raw/MEME/RankLinear2.0_40_unc-30/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/unc-30.fasta model: mod= zoops nmotifs= 5 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 8 maxw= 8 nsites: minsites= 2 maxsites= 62 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 4960 N= 62 sample: seed= 0 hsfrac= 0 searchsize= 4960 norand= no csites= 1000 Letter frequencies in dataset: A 0.29 C 0.196 G 0.217 T 0.298 Background letter frequencies (from file dataset with add-one prior applied): A 0.29 C 0.196 G 0.217 T 0.298 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GCTGGCGC MEME-1 width = 8 sites = 5 llr = 58 E-value = 8.6e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCTGGCGC MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C :a:::a:8 probability G a::aa:a: matrix T ::a::::2 bits 2.4 * * 2.1 ** **** 1.9 ** **** 1.6 ******* Relative 1.4 ******** Entropy 1.2 ******** (16.8 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GCTGGCGC consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCTGGCGC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:2177689-2177769 55 4.98e-06 AAGGCCTCTT GCTGGCGC ACTCGAGGAT chrII:411000-411080 62 4.98e-06 AAGGGAGACT GCTGGCGC ATTTCTTGAT chrI:11517247-11517327 63 4.98e-06 ACCAGTGGTT GCTGGCGC GTTTCTCGTG chrII:7945300-7945380 42 4.98e-06 AAGGACGCAT GCTGGCGC AAAGTGTCTT chrIII:13466366-13466446 39 1.25e-05 AGGAGTGGTT GCTGGCGT ACTTTGCGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCTGGCGC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:2177689-2177769 5e-06 54_[+1]_18 chrII:411000-411080 5e-06 61_[+1]_11 chrI:11517247-11517327 5e-06 62_[+1]_10 chrII:7945300-7945380 5e-06 41_[+1]_31 chrIII:13466366-13466446 1.3e-05 38_[+1]_34 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCTGGCGC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCTGGCGC width=8 seqs=5 chrIV:2177689-2177769 ( 55) GCTGGCGC 1 chrII:411000-411080 ( 62) GCTGGCGC 1 chrI:11517247-11517327 ( 63) GCTGGCGC 1 chrII:7945300-7945380 ( 42) GCTGGCGC 1 chrIII:13466366-13466446 ( 39) GCTGGCGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCTGGCGC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4526 bayes= 10.0723 E= 8.6e+000 -897 -897 220 -897 -897 235 -897 -897 -897 -897 -897 175 -897 -897 220 -897 -897 -897 220 -897 -897 235 -897 -897 -897 -897 220 -897 -897 203 -897 -57 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCTGGCGC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 8.6e+000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.000000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCTGGCGC MEME-1 regular expression -------------------------------------------------------------------------------- GCTGGCG[CT] -------------------------------------------------------------------------------- Time 0.80 secs. ******************************************************************************** ******************************************************************************** MOTIF RCGCMRAG MEME-2 width = 8 sites = 11 llr = 101 E-value = 6.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif RCGCMRAG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 5:::64a: pos.-specific C :a:a4::3 probability G 5:a::6:7 matrix T :::::::: bits 2.4 * * 2.1 *** 1.9 *** * 1.6 *** * Relative 1.4 *** ** Entropy 1.2 *** *** (13.3 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GCGCAGAG consensus A CA C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCGCMRAG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:2725927-2726007 29 1.20e-05 ATGATAAAAC GCGCCGAG AAACGCGCCA chrIII:13061296-13061376 6 2.16e-05 GAGAT ACGCAGAG AAGCATACAA chrIV:15471544-15471624 72 2.16e-05 AGAGTACGAG ACGCAGAG A chrIV:1070516-1070596 28 2.16e-05 CCAGCATGAG ACGCAGAG AGTCGCAGCG chrI:13495264-13495344 50 2.16e-05 gaggggagag acgcagag aaaagagaga chrII:411000-411080 47 4.41e-05 GAATGCTTGC GCGCAAAG GGAGACTGCT chrI:17002-17082 47 4.41e-05 CACGAGAAAT GCGCAAAG GCTAAATTCG chrIV:2177689-2177769 40 5.49e-05 CACCGGGAAT GCGCCAAG GCCTCTTGCT chrIII:10634167-10634247 61 5.49e-05 CCCTGGGTAG GCGCCGAC TTGCACCCGC chrI:8786917-8786997 58 7.64e-05 AGACATAGAG ACGCAGAC AATCAGGGAG chrI:11517247-11517327 47 1.05e-04 TTCACGAAAC GCGCCAAC CAGTGGTTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCGCMRAG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:2725927-2726007 1.2e-05 28_[+2]_44 chrIII:13061296-13061376 2.2e-05 5_[+2]_67 chrIV:15471544-15471624 2.2e-05 71_[+2]_1 chrIV:1070516-1070596 2.2e-05 27_[+2]_45 chrI:13495264-13495344 2.2e-05 49_[+2]_23 chrII:411000-411080 4.4e-05 46_[+2]_26 chrI:17002-17082 4.4e-05 46_[+2]_26 chrIV:2177689-2177769 5.5e-05 39_[+2]_33 chrIII:10634167-10634247 5.5e-05 60_[+2]_12 chrI:8786917-8786997 7.6e-05 57_[+2]_15 chrI:11517247-11517327 0.00011 46_[+2]_26 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCGCMRAG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RCGCMRAG width=8 seqs=11 chrIV:2725927-2726007 ( 29) GCGCCGAG 1 chrIII:13061296-13061376 ( 6) ACGCAGAG 1 chrIV:15471544-15471624 ( 72) ACGCAGAG 1 chrIV:1070516-1070596 ( 28) ACGCAGAG 1 chrI:13495264-13495344 ( 50) ACGCAGAG 1 chrII:411000-411080 ( 47) GCGCAAAG 1 chrI:17002-17082 ( 47) GCGCAAAG 1 chrIV:2177689-2177769 ( 40) GCGCCAAG 1 chrIII:10634167-10634247 ( 61) GCGCCGAC 1 chrI:8786917-8786997 ( 58) ACGCAGAC 1 chrI:11517247-11517327 ( 47) GCGCCAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCGCMRAG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4526 bayes= 9.70934 E= 6.4e+000 65 -1010 133 -1010 -1010 235 -1010 -1010 -1010 -1010 220 -1010 -1010 235 -1010 -1010 113 89 -1010 -1010 33 -1010 155 -1010 179 -1010 -1010 -1010 -1010 48 174 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCGCMRAG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 11 E= 6.4e+000 0.454545 0.000000 0.545455 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.636364 0.363636 0.000000 0.000000 0.363636 0.000000 0.636364 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.272727 0.727273 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCGCMRAG MEME-2 regular expression -------------------------------------------------------------------------------- [GA]CGC[AC][GA]A[GC] -------------------------------------------------------------------------------- Time 1.42 secs. ******************************************************************************** ******************************************************************************** MOTIF GAAAAANA MEME-3 width = 8 sites = 32 llr = 216 E-value = 3.0e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAAAAANA MEME-3 Description -------------------------------------------------------------------------------- Simplified A :aa8953a pos.-specific C 3:::112: probability G 8::2:23: matrix T :::::23: bits 2.4 2.1 1.9 ** * 1.6 ** * Relative 1.4 *** * * Entropy 1.2 ***** * (9.7 bits) 0.9 ***** * 0.7 ***** * 0.5 ***** * 0.2 ****** * 0.0 -------- Multilevel GAAAAAGA consensus C TT sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAAAANA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrI:10033694-10033774 39 2.80e-05 aggagaaaat gaaaaaga agagagcaca chrV:4468462-4468542 10 2.80e-05 ATGATGAGA GAAAAAGA GCTAAAATAA chrIV:17281424-17281504 64 9.18e-05 GAATAAAAAT GAAAAATA CATTGATCG chrII:3270702-3270782 67 9.18e-05 CTCCCCTTCT GAAAAATA CATTCC chrX:4095126-4095206 16 9.18e-05 TTTCCTGAAA GAAAAATA ATAATTTTTT chrIV:15471544-15471624 6 1.29e-04 GAAAA GAAAAAAA AACAGGGAAG chrI:7952195-7952275 49 1.29e-04 TATAATAAAT GAAAAAAA AAGAAGAAGA chrII:14427890-14427970 35 1.29e-04 TGAGTAAATT GAAAAAAA GGGAGGGGGG chrIV:14034130-14034210 43 1.50e-04 GAGAAATGAG GAAAAGGA AGAAATATGT chrIV:7899066-7899146 69 1.50e-04 GAAATGAGAC GAAAAGGA TTAG chrII:7945300-7945380 3 1.79e-04 GA GAAAATGA ATAAAATGAC chrX:13913845-13913925 34 2.52e-04 AGCTTTTCTG GAAAAGTA GATGACGAGG chrIII:5571237-5571317 32 2.52e-04 ATACAAGAGA GAAAAGTA ATCCCACTCG chrI:17002-17082 70 3.45e-04 ATTCGGCGCG GAAAATCA TTT chrII:156129-156209 48 3.45e-04 CAAAGTGCGC GAAAATTA AATGTTTTTT chrI:11517247-11517327 5 4.42e-04 CCTG CAAAAATA TTCTAATTTG chrV:265214-265294 48 4.42e-04 CATAGGCAAC CAAAAATA TTTTCCAAGT chrIII:13061296-13061376 21 4.42e-04 GAGAAGCATA CAAAAACA AACTGTCAAG chrIII:10881844-10881924 1 4.42e-04 . CAAAAACA AGGCCATAAA chrI:1691548-1691628 27 4.96e-04 AACTCGTCTT GAAGAAGA CGTCGGCGGT chrI:12170852-12170932 55 4.96e-04 GGGAAAATAG GAAGAAGA CAAATTGGTG chrII:13237916-13237996 49 6.10e-04 AACAAATAGA GAAGAAAA CAACCAAAAA chrIV:11765749-11765829 25 6.10e-04 GAGAAAGAAG GAAGAAAA CATTTGCTTT chrV:10356110-10356190 43 6.36e-04 CCATATGTAG CAAAATGA GCGGAAATTC chrII:1233092-1233172 38 7.22e-04 TTTTTTTTTT GAAAACCA CTATATATCA chrI:13514361-13514441 59 7.88e-04 GCGCTTGCTC GAAAACAA TTTGAATTGA chrI:13495264-13495344 15 7.88e-04 TGGCTGGGAG CAAAAGAA GAAGCTTCTA chrIII:13466366-13466446 11 8.48e-04 CTTAGCTTCA CAAAATCA ATATGCGTCA chrV:5201851-5201931 48 9.23e-04 TGGAGGATTA GAAACAGA ATACAAGGGA chrIV:2725927-2726007 9 9.23e-04 ATAGGAAA CAAAATAA TAATGATAAA chrI:11140623-11140703 27 9.77e-04 AGAGGATGGA GAAGAGCA CATCAAATTT chrIV:1057899-1057979 48 1.59e-03 CGAGACCCAT GAAACTTA TATTTTTGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAAAANA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrI:10033694-10033774 2.8e-05 38_[+3]_34 chrV:4468462-4468542 2.8e-05 9_[+3]_63 chrIV:17281424-17281504 9.2e-05 63_[+3]_9 chrII:3270702-3270782 9.2e-05 66_[+3]_6 chrX:4095126-4095206 9.2e-05 15_[+3]_57 chrIV:15471544-15471624 0.00013 5_[+3]_67 chrI:7952195-7952275 0.00013 48_[+3]_24 chrII:14427890-14427970 0.00013 34_[+3]_38 chrIV:14034130-14034210 0.00015 42_[+3]_30 chrIV:7899066-7899146 0.00015 68_[+3]_4 chrII:7945300-7945380 0.00018 2_[+3]_70 chrX:13913845-13913925 0.00025 33_[+3]_39 chrIII:5571237-5571317 0.00025 31_[+3]_41 chrI:17002-17082 0.00035 69_[+3]_3 chrII:156129-156209 0.00035 47_[+3]_25 chrI:11517247-11517327 0.00044 4_[+3]_68 chrV:265214-265294 0.00044 47_[+3]_25 chrIII:13061296-13061376 0.00044 20_[+3]_52 chrIII:10881844-10881924 0.00044 [+3]_72 chrI:1691548-1691628 0.0005 26_[+3]_46 chrI:12170852-12170932 0.0005 54_[+3]_18 chrII:13237916-13237996 0.00061 48_[+3]_24 chrIV:11765749-11765829 0.00061 24_[+3]_48 chrV:10356110-10356190 0.00064 42_[+3]_30 chrII:1233092-1233172 0.00072 37_[+3]_35 chrI:13514361-13514441 0.00079 58_[+3]_14 chrI:13495264-13495344 0.00079 14_[+3]_58 chrIII:13466366-13466446 0.00085 10_[+3]_62 chrV:5201851-5201931 0.00092 47_[+3]_25 chrIV:2725927-2726007 0.00092 8_[+3]_64 chrI:11140623-11140703 0.00098 26_[+3]_46 chrIV:1057899-1057979 0.0016 47_[+3]_25 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAAAANA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GAAAAANA width=8 seqs=32 chrI:10033694-10033774 ( 39) GAAAAAGA 1 chrV:4468462-4468542 ( 10) GAAAAAGA 1 chrIV:17281424-17281504 ( 64) GAAAAATA 1 chrII:3270702-3270782 ( 67) GAAAAATA 1 chrX:4095126-4095206 ( 16) GAAAAATA 1 chrIV:15471544-15471624 ( 6) GAAAAAAA 1 chrI:7952195-7952275 ( 49) GAAAAAAA 1 chrII:14427890-14427970 ( 35) GAAAAAAA 1 chrIV:14034130-14034210 ( 43) GAAAAGGA 1 chrIV:7899066-7899146 ( 69) GAAAAGGA 1 chrII:7945300-7945380 ( 3) GAAAATGA 1 chrX:13913845-13913925 ( 34) GAAAAGTA 1 chrIII:5571237-5571317 ( 32) GAAAAGTA 1 chrI:17002-17082 ( 70) GAAAATCA 1 chrII:156129-156209 ( 48) GAAAATTA 1 chrI:11517247-11517327 ( 5) CAAAAATA 1 chrV:265214-265294 ( 48) CAAAAATA 1 chrIII:13061296-13061376 ( 21) CAAAAACA 1 chrIII:10881844-10881924 ( 1) CAAAAACA 1 chrI:1691548-1691628 ( 27) GAAGAAGA 1 chrI:12170852-12170932 ( 55) GAAGAAGA 1 chrII:13237916-13237996 ( 49) GAAGAAAA 1 chrIV:11765749-11765829 ( 25) GAAGAAAA 1 chrV:10356110-10356190 ( 43) CAAAATGA 1 chrII:1233092-1233172 ( 38) GAAAACCA 1 chrI:13514361-13514441 ( 59) GAAAACAA 1 chrI:13495264-13495344 ( 15) CAAAAGAA 1 chrIII:13466366-13466446 ( 11) CAAAATCA 1 chrV:5201851-5201931 ( 48) GAAACAGA 1 chrIV:2725927-2726007 ( 9) CAAAATAA 1 chrI:11140623-11140703 ( 27) GAAGAGCA 1 chrIV:1057899-1057979 ( 48) GAAACTTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAAAANA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4526 bayes= 7.87485 E= 3.0e-002 -1164 35 179 -1164 179 -1164 -1164 -1164 179 -1164 -1164 -1164 154 -1164 -47 -1164 169 -165 -1164 -1164 87 -165 -21 -44 -21 -6 37 -8 179 -1164 -1164 -1164 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAAAANA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 3.0e-002 0.000000 0.250000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.843750 0.000000 0.156250 0.000000 0.937500 0.062500 0.000000 0.000000 0.531250 0.062500 0.187500 0.218750 0.250000 0.187500 0.281250 0.281250 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAAAANA MEME-3 regular expression -------------------------------------------------------------------------------- [GC]AAAA[AT][GTA]A -------------------------------------------------------------------------------- Time 2.05 secs. ******************************************************************************** ******************************************************************************** MOTIF GHKTCTCB MEME-4 width = 8 sites = 14 llr = 118 E-value = 6.5e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GHKTCTCB MEME-4 Description -------------------------------------------------------------------------------- Simplified A :3:::::: pos.-specific C :4::a:a3 probability G a16::::4 matrix T :34a:a:4 bits 2.4 * * 2.1 * * * 1.9 * * * 1.6 * **** Relative 1.4 * **** Entropy 1.2 * **** (12.1 bits) 0.9 * ***** 0.7 * ***** 0.5 * ****** 0.2 ******** 0.0 -------- Multilevel GCGTCTCG consensus AT T sequence T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GHKTCTCB MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:12612578-12612658 38 1.30e-05 GTGTTCTCTG GCGTCTCC ACAATCTGTA chrI:17002-17082 5 2.24e-05 CTCT GCGTCTCT CACCCTTCAG chrIII:13061296-13061376 45 2.24e-05 CAAGCTATCT GCGTCTCT GTCGTTGTTT chrI:13514361-13514441 16 2.24e-05 TCAACTCTCT GCGTCTCT ACTCTCTACG chrII:411000-411080 10 5.23e-05 AAATTCTTA GCTTCTCG CGCTTTTTCA chrIV:14464276-14464356 21 5.23e-05 TTTCCGCTTT GAGTCTCG CACGGAAGAG chrIV:14033232-14033312 31 1.20e-04 ATCGCTCTGT GAGTCTCT GCCTCTTAGT chrIII:13466366-13466446 65 1.20e-04 ATGTTTGTTT GTGTCTCT CAAATCTC chrI:27165-27245 42 1.48e-04 gaattAATCG GATTCTCG TAGTTTATTT chrI:11517247-11517327 71 1.48e-04 TTGCTGGCGC GTTTCTCG TG chrV:9175423-9175503 29 1.74e-04 TGTTTTTCGC GTTTCTCC GTTGCGActt chrX:11137844-11137924 40 1.74e-04 TCTCCGTGCA GATTCTCC CACTTCTTTC chrV:1471779-1471859 48 1.74e-04 TCTTTTTTTT GTTTCTCC GTCAATTTTC chrII:8185168-8185248 31 2.20e-04 AGCTGGTGTT GGGTCTCG GCACGATTAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GHKTCTCB MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:12612578-12612658 1.3e-05 37_[+4]_35 chrI:17002-17082 2.2e-05 4_[+4]_68 chrIII:13061296-13061376 2.2e-05 44_[+4]_28 chrI:13514361-13514441 2.2e-05 15_[+4]_57 chrII:411000-411080 5.2e-05 9_[+4]_63 chrIV:14464276-14464356 5.2e-05 20_[+4]_52 chrIV:14033232-14033312 0.00012 30_[+4]_42 chrIII:13466366-13466446 0.00012 64_[+4]_8 chrI:27165-27245 0.00015 41_[+4]_31 chrI:11517247-11517327 0.00015 70_[+4]_2 chrV:9175423-9175503 0.00017 28_[+4]_44 chrX:11137844-11137924 0.00017 39_[+4]_33 chrV:1471779-1471859 0.00017 47_[+4]_25 chrII:8185168-8185248 0.00022 30_[+4]_42 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GHKTCTCB MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GHKTCTCB width=8 seqs=14 chrIII:12612578-12612658 ( 38) GCGTCTCC 1 chrI:17002-17082 ( 5) GCGTCTCT 1 chrIII:13061296-13061376 ( 45) GCGTCTCT 1 chrI:13514361-13514441 ( 16) GCGTCTCT 1 chrII:411000-411080 ( 10) GCTTCTCG 1 chrIV:14464276-14464356 ( 21) GAGTCTCG 1 chrIV:14033232-14033312 ( 31) GAGTCTCT 1 chrIII:13466366-13466446 ( 65) GTGTCTCT 1 chrI:27165-27245 ( 42) GATTCTCG 1 chrI:11517247-11517327 ( 71) GTTTCTCG 1 chrV:9175423-9175503 ( 29) GTTTCTCC 1 chrX:11137844-11137924 ( 40) GATTCTCC 1 chrV:1471779-1471859 ( 48) GTTTCTCC 1 chrII:8185168-8185248 ( 31) GGGTCTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GHKTCTCB MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4526 bayes= 9.55714 E= 6.5e+001 -1045 -1045 220 -1045 -2 87 -160 -6 -1045 -1045 140 53 -1045 -1045 -1045 175 -1045 235 -1045 -1045 -1045 -1045 -1045 175 -1045 235 -1045 -1045 -1045 55 72 26 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GHKTCTCB MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 14 E= 6.5e+001 0.000000 0.000000 1.000000 0.000000 0.285714 0.357143 0.071429 0.285714 0.000000 0.000000 0.571429 0.428571 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.285714 0.357143 0.357143 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GHKTCTCB MEME-4 regular expression -------------------------------------------------------------------------------- G[CAT][GT]TCTC[GTC] -------------------------------------------------------------------------------- Time 2.64 secs. ******************************************************************************** ******************************************************************************** MOTIF SASCGCGC MEME-5 width = 8 sites = 4 llr = 42 E-value = 1.3e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif SASCGCGC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :a:::::: pos.-specific C 5:5a:a3a probability G 5:5:a:8: matrix T :::::::: bits 2.4 * * * 2.1 *** * 1.9 * *** * 1.6 * *** * Relative 1.4 * ***** Entropy 1.2 ******** (15.0 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CACCGCGC consensus G G C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SASCGCGC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:2177689-2177769 73 3.95e-06 ACTCGAGGAT CACCGCGC chrIII:1202352-1202432 24 1.27e-05 GGTGTTTGCG GACCGCGC GGTGTTTGCG chrI:13514361-13514441 45 1.75e-05 CGTGGCGGTG GAGCGCGC TTGCTCGAAA chrIV:1070516-1070596 41 2.90e-05 CAGAGAGTCG CAGCGCCC CGGCGAGAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SASCGCGC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:2177689-2177769 4e-06 72_[+5] chrIII:1202352-1202432 1.3e-05 23_[+5]_49 chrI:13514361-13514441 1.8e-05 44_[+5]_28 chrIV:1070516-1070596 2.9e-05 40_[+5]_32 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SASCGCGC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF SASCGCGC width=8 seqs=4 chrIV:2177689-2177769 ( 73) CACCGCGC 1 chrIII:1202352-1202432 ( 24) GACCGCGC 1 chrI:13514361-13514441 ( 45) GAGCGCGC 1 chrIV:1070516-1070596 ( 41) CAGCGCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SASCGCGC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4526 bayes= 10.8802 E= 1.3e+004 -865 135 120 -865 178 -865 -865 -865 -865 135 120 -865 -865 235 -865 -865 -865 -865 220 -865 -865 235 -865 -865 -865 35 179 -865 -865 235 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SASCGCGC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 1.3e+004 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SASCGCGC MEME-5 regular expression -------------------------------------------------------------------------------- [CG]A[CG]CGC[GC]C -------------------------------------------------------------------------------- Time 3.22 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:5054449-5054529 9.51e-01 80 chrX:2604759-2604839 3.75e-01 80 chrII:14427890-14427970 3.94e-01 80 chrIII:5571237-5571317 5.00e-01 80 chrI:13495264-13495344 1.28e-02 49_[+2(2.16e-05)]_23 chrIV:1070516-1070596 1.09e-04 27_[+2(2.16e-05)]_5_[+5(2.90e-05)]_\ 32 chrX:3898588-3898668 9.26e-01 80 chrIV:1057899-1057979 5.46e-01 80 chrIV:7899066-7899146 7.34e-02 80 chrV:4775283-4775363 8.12e-01 80 chrI:7952195-7952275 1.64e-01 80 chrV:4468462-4468542 1.94e-01 9_[+3(2.80e-05)]_63 chrIII:13466366-13466446 2.07e-04 38_[+1(1.25e-05)]_34 chrX:4095126-4095206 1.34e-01 15_[+3(9.18e-05)]_57 chrII:3270702-3270782 6.82e-02 66_[+3(9.18e-05)]_6 chrIV:2725927-2726007 1.38e-04 28_[+2(1.20e-05)]_44 chrV:1471779-1471859 4.96e-01 80 chrIV:14033232-14033312 5.50e-02 80 chrIV:9811695-9811775 3.23e-01 80 chrI:10033694-10033774 2.44e-02 38_[+3(2.80e-05)]_34 chrIV:11765749-11765829 3.19e-01 80 chrIV:17281424-17281504 2.90e-01 63_[+3(9.18e-05)]_9 chrX:13913845-13913925 1.01e-01 80 chrI:13514361-13514441 1.38e-05 15_[+4(2.24e-05)]_21_[+5(1.75e-05)]_\ 28 chrII:156129-156209 3.07e-02 80 chrX:11137844-11137924 2.87e-02 80 chrII:13237916-13237996 5.43e-01 80 chrIV:14464276-14464356 1.89e-02 20_[+4(5.23e-05)]_52 chrV:5201851-5201931 6.69e-01 80 chrI:12170852-12170932 1.78e-01 80 chrV:6224582-6224662 2.25e-01 80 chrIII:1202352-1202432 2.27e-02 23_[+5(1.27e-05)]_49 chrI:7370268-7370348 8.73e-01 80 chrI:11140623-11140703 3.37e-01 80 chrV:18079287-18079367 6.52e-01 80 chrI:8786917-8786997 1.68e-01 57_[+2(7.64e-05)]_15 chrI:1691548-1691628 1.65e-01 80 chrII:1233092-1233172 7.31e-01 80 chrIV:443759-443839 9.41e-01 80 chrV:18087022-18087102 9.16e-01 80 chrII:7945300-7945380 3.67e-06 41_[+1(4.98e-06)]_31 chrIV:12724765-12724845 6.85e-01 80 chrIII:10881844-10881924 3.15e-01 80 chrIV:15471544-15471624 1.71e-03 71_[+2(2.16e-05)]_1 chrIII:13061296-13061376 8.47e-05 5_[+2(2.16e-05)]_31_[+4(2.24e-05)]_\ 28 chrI:17002-17082 7.07e-06 4_[+4(2.24e-05)]_34_[+2(4.41e-05)]_\ 26 chrV:904827-904907 7.86e-01 80 chrV:265214-265294 2.13e-01 80 chrX:949603-949683 6.25e-01 80 chrII:8185168-8185248 5.95e-02 80 chrI:11517247-11517327 8.60e-07 62_[+1(4.98e-06)]_10 chrIII:10634167-10634247 2.19e-03 60_[+2(5.49e-05)]_12 chrII:411000-411080 1.08e-06 9_[+4(5.23e-05)]_29_[+2(4.41e-05)]_\ 7_[+1(4.98e-06)]_11 chrI:27165-27245 3.11e-01 80 chrV:10356110-10356190 2.21e-01 80 chrIV:14034130-14034210 4.08e-01 80 chrIV:2177689-2177769 1.48e-06 39_[+2(5.49e-05)]_7_[+1(4.98e-06)]_\ 10_[+5(3.95e-06)] chrI:535370-535450 6.42e-02 80 chrIII:12612578-12612658 1.47e-02 37_[+4(1.30e-05)]_35 chrII:6951536-6951616 5.36e-01 80 chrV:9175423-9175503 2.27e-01 80 chrV:5592443-5592523 4.95e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n11.farnam.hpc.yale.internal ********************************************************************************